Structure of PDB 3cqz Chain A

Receptor sequence
>3cqzA (length=1349) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETAKIGGLNDPRLGSID
RNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGK
LLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLV
SRGGCGNTQPTIRKDGLKLVGSWKKEPELRVLSTEEILNIFKHISVKDFT
SLGFNEVFSRPEWMILTCLPVPPPPVRPTFKLADILKANISLETLEHNGA
PHHAIEEAESLLQFHVATYMDFSARTVISGDPNLELDQVGVPKSIAKTLT
YPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQ
LQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVT
SPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQ
DTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGK
QILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSS
NGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPT
MREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEA
RDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRI
AFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLI
DTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDA
AHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKL
QVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDH
TKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSR
LATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEP
ATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHA
ADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFS
LLDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDND
EKLIIRCRVVEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVP
SPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIE
AGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGMRCS
FEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESL
3D structure
PDB3cqz The RNA Polymerase II Trigger Loop Functions in Substrate Selection and is Directly Targeted by Alpha-Amanitin.
ChainA
Resolution2.8 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485 H1085
Catalytic site (residue number reindexed from 1) D406 D408 D410 H1010
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 peptide A N723 R726 I756 A759 Q760 V765 G766 Q767 Q768 S769 G772 R774 H816 G819 E822 H1085 N648 R651 I681 A684 Q685 V690 G691 Q692 Q693 S694 G697 R699 H741 G744 E747 H1010
BS02 ZN A C107 C110 C148 C167 C95 C98 C136 C155
BS03 ZN A C70 C77 H80 C58 C65 H68
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
GO:0019985 translesion synthesis
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3cqz, PDBe:3cqz, PDBj:3cqz
PDBsum3cqz
PubMed18538653
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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